Recently, I had to change the AD import connection for my Sharepoint user profiles. I noticed after this change the audience memberships were not compiling. I searched the web and found nothing exactly solving this issue. Many of my audiences are based on groups in AD. I checked the rules again and found when I brought up the browser to select users/groups, the groups were all listed twice or even three times.
Temporary fix: I had to select the bottom most listing to get the audience to have members again. I am not sure why it is doing this. There must be some purge tool which can clear out the list of groups and then rebuild, but I haven't found it yet.
Thought I would pass this along in case anyone else is encountering this same issue.